…
SpatialData 0.99.0
library(tidyr)
library(ggplot2)
library(patchwork)
library(SpatialData)
library(SingleCellExperiment)
path <- file.path("..", "inst", "extdata", "mibitof")
(spd <- readSpatialData(path))
## class: SpatialData
## table: 36 3309
## images(3): point16_image point23_image point8_image
## labels(3): point16_labels point23_labels point8_labels
## shapes(0):
## points(0):
## coords(0):
ps <- lapply(images(spd), plotElement)
wrap_plots(ps, nrow = 1)
ps <- lapply(labels(spd), plotElement)
wrap_plots(ps, nrow = 1)
ps <- mapply(
\(i, l) plotSD(spd, image = i, label = l),
SIMPLIFY = FALSE, i = imageNames(spd), l = labelNames(spd))
wrap_plots(ps, nrow = 1)
# TODO: one function call should aggregate
# across all matching coordinate systems
ms <- mapply(
\(i, l) {
sce <- aggregateImage(spd, image = i, label = l)
sce$id <- i; return(sce)
},
SIMPLIFY = FALSE, i = imageNames(spd), l = labelNames(spd))
(sce <- do.call(cbind, ms))
## class: SingleCellExperiment
## dim: 3 3771
## metadata(0):
## assays(1): mean
## rownames: NULL
## rowData names(0):
## colnames(3771): 1 2 ... 1180 1181
## colData names(3): x y id
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
chs <- rownames(sce) <- c("R", "G", "B")
df <- data.frame(colData(sce), t(assay(sce)), check.names = FALSE)
fd <- pivot_longer(df, all_of(chs))
fd$name <- factor(fd$name, chs)
ggplot(fd, aes(x, y, col = value)) +
geom_point(size = 1) + facet_grid(id ~ name) +
scale_color_viridis_c(option = "C", trans = "sqrt") +
coord_equal() + theme_linedraw() + theme(
axis.title = element_blank(),
panel.grid = element_blank(),
panel.background = element_rect(fill = "black"),
strip.background = element_rect(fill = "black", color = "white"))
sessionInfo()
## R version 4.3.0 (2023-04-21)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.2.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: Europe/Zurich
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics utils stats4 methods base
##
## other attached packages:
## [1] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.1
## [3] Biobase_2.60.0 GenomicRanges_1.52.0
## [5] GenomeInfoDb_1.36.0 IRanges_2.34.0
## [7] S4Vectors_0.38.1 BiocGenerics_0.46.0
## [9] MatrixGenerics_1.12.0 matrixStats_0.63.0
## [11] SpatialData_0.99.0 patchwork_1.1.2
## [13] ggplot2_3.4.2 tidyr_1.3.0
## [15] BiocStyle_2.28.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.0 viridisLite_0.4.2 EBImage_4.42.0
## [4] farver_2.1.1 dplyr_1.1.2 filelock_1.0.2
## [7] arrow_11.0.0.3 R.utils_2.12.2 bitops_1.0-7
## [10] fastmap_1.1.1 RCurl_1.98-1.12 digest_0.6.31
## [13] lifecycle_1.0.3 paws.storage_0.2.0 magrittr_2.0.3
## [16] compiler_4.3.0 rlang_1.1.1 sass_0.4.6
## [19] tools_4.3.0 utf8_1.2.3 yaml_2.3.7
## [22] knitr_1.42 labeling_0.4.2 S4Arrays_1.0.1
## [25] htmlwidgets_1.6.2 bit_4.0.5 curl_5.0.0
## [28] here_1.0.1 reticulate_1.28 DelayedArray_0.26.1
## [31] abind_1.4-5 zellkonverter_1.10.0 withr_2.5.0
## [34] purrr_1.0.1 R.oo_1.25.0 grid_4.3.0
## [37] fansi_1.0.4 grDevices_4.3.0 colorspace_2.1-0
## [40] scales_1.2.1 cli_3.6.1 rmarkdown_2.21
## [43] crayon_1.5.2 generics_0.1.3 rstudioapi_0.14
## [46] httr_1.4.5 cachem_1.0.8 stringr_1.5.0
## [49] zlibbioc_1.46.0 datasets_4.3.0 parallel_4.3.0
## [52] assertthat_0.2.1 BiocManager_1.30.20 XVector_0.40.0
## [55] tiff_0.1-11 basilisk_1.12.0 vctrs_0.6.2
## [58] Matrix_1.5-4 dir.expiry_1.8.0 jsonlite_1.8.4
## [61] bookdown_0.33 fftwtools_0.9-11 bit64_4.0.5
## [64] magick_2.7.4 jpeg_0.1-10 locfit_1.5-9.7
## [67] jquerylib_0.1.4 glue_1.6.2 codetools_0.2-19
## [70] stringi_1.7.12 gtable_0.3.3 Rarr_1.0.0
## [73] munsell_0.5.0 tibble_3.2.1 pillar_1.9.0
## [76] basilisk.utils_1.12.0 htmltools_0.5.5 GenomeInfoDbData_1.2.10
## [79] R6_2.5.1 rprojroot_2.0.3 evaluate_0.21
## [82] lattice_0.21-8 highr_0.10 R.methodsS3_1.8.2
## [85] png_0.1-8 paws.common_0.5.6 bslib_0.4.2
## [88] Rcpp_1.0.10 xfun_0.39 pkgconfig_2.0.3